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DOP089 Comparative genome analysis of Crohn's Disease-associated adherent, invasive Escherichia coli fails to detect a common molecular property

C. O'Brien*1, 2, P. Pavli1, 2, D. Gordon3, K. Holt4, A. Dubois5, A. Darfeuille-Michaud5, M. Agnes-Bringer5

1Australian National University, Medical School, Canberra, ACT, Australia, 2Canberra Hospital, Gastroenterology and Hepatology Unit, Canberra, ACT, Australia, 3Australian National University, Research School of Biology, Canberra, ACT, Australia, 4University of Melbourne, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia, 5University of Auvergne, Pathogenie Bacterienne Intestinale, Clermont-Ferrand, France

Background

Adherent-invasive E. coli (AIEC) are a leading candidate bacterial trigger for Crohn's disease (CD). The AIEC phenotype is based on a strain's ability (i) to adhere to and invade epithelial cells (ECs), and (ii) to survive and replicate within macrophages. No defining molecular features have been identified for AIEC and phenotypic testing is the only way to identify them. The aim of this study was to identify a common molecular property of the AIEC phenotype.

Methods

The whole genomes of 41 B2 phylogroup E. coli strains, isolated from 19 patients with inflammatory bowel disease (IBD [14 with CD, 5 with ulcerative colitis]), and 17 without IBD, were sequenced using the Illumina HiSeq 2000 platform. Adherence/invasion assays were conducted using I-407 ECs and survival/replication assays using THP-1 macrophages. The genomes were assembled in CLC workbench and annotated in Genoscope. Protein cluster analysis was conducted using CD-HIT. The resulting matrices were analysed in R to determine genes unique/more frequent in AIEC strains compared to non-AIEC strains. The Harvest software suite was used to detect SNPs and generate core-genome phylogenies.

Results

12/41 strains displayed the AIEC phenotype (5 CD, 2 UC, 5 non-IBD). The AIEC strains were scattered throughout the phylogenetic tree and we did not identify a gene in common to all, or the majority of, AIEC isolates despite restricting the analysis to B2 phylogroup strains. For patients 12 and 55, we isolated two strains that were highly similar (same sequence type), differing by just 127 and 341 genes, respectively. One strain from each patient displayed the AIEC phenotype, the other did not. None of the genes, or SNPs, observed in the AIEC strain was observed in all, or the majority of, other AIEC strains.

Conclusion

Comparative genomic analysis of AIEC and non-AIEC strains failed to detect a molecular property exclusive to the AIEC phenotype. Our Results indicate that multiple sets of genes, and/or regulatory differences, contribute to the AIEC phenotype.